GBIF and rgbif introduction (Nordic Oikos 2018)

Nordic Oikos 2018 - R workshop

Scientific reuse of openly published biodiversity information: Programmatic access to and analysis of primary biodiversity information using R. Nordic Oikos 2018, pre-conference R workshop, 18 and 19 February 2018. Further information here.

Session 1 includes brief examples of accessing GBIF data from R using the rgbif package from rOpenSci. See session 3 for more examples.

Choose a species name

require(rgbif) # r-package for GBIF data
sp_name <- "Hepatica nobilis" # liverleaf (blaaveis:no)
key <- name_backbone(name=sp_name, kingdom="Plantae")$speciesKey

Retrieve GBIF species occurrence data

require(rgbif) # r-package for GBIF data
sp <- occ_search(taxonKey=key, return="data", hasCoordinate=TRUE, limit=200) 
gbifmap(sp)

Map of Hepatica nobilis occurrences

Retrieve GBIF species occurrence data from Trondheim

Species is Hepatica nobilis with taxonKey 5371699

require('rgbif') # r-package for GBIF data
require('mapr') # rOpenSci r-package for mapping (occurrence data)
bbox <- c(10.2,63.3,10.6,63.5) # Trondheim
sp_bb <- occ_search(taxonKey=key, return="data", hasCoordinate=TRUE, country="NO", geometry=bbox, limit=200) 
map_leaflet(sp_bb, "decimalLongitude", "decimalLatitude", size=3, color="blue")

Leaflet map

Extract coordinates suitable for e.g. Maxent

xy <- sp[c("decimalLongitude","decimalLatitude")] ## Extract only the coordinates
sp_xy <- sp[c("species", "decimalLongitude","decimalLatitude")] ## Input format for Maxent
head(sp_xy, n=5) ## preview first 5 records

Write dataframe to file (useful for Maxent etc)

write.table(sp_xy, file="./demo_data/sp_xy.txt", sep="\t", row.names=FALSE, qmethod="double") ## for Maxent

Read data file back into R

sp_xy <- read.delim("./demo_data/sp_xy.txt", header=TRUE, dec=".", stringsAsFactors=FALSE)

---

GBIF demo examples for species: Hepatica nobilis (taxonKey:5371699).

This script uses R Markdown